At least 10 pro-Palestinian activists were killed and dozens injured in a battle at sea with Israeli naval commandos today, sparking an international diplomatic crisis and the prospect of angry demonstrations across Israel, the Palestinian territories, Turkey and beyond.

Dozens of activists injured during the storming of a Gaza aid flotilla were ferried to hospitals in Tel Aviv, Haifa and Ashkelon. The Israeli military said at least five of its personnel were also injured, at least one seriously.

The incident engulfed Israel in a war of words with its ally Turkey, with whom relations were already stained following the Israelis three-week military assault on the Gaza Strip in 2008-9. Today's deaths and injuries were condemned by the UN, EU and other countries.

The Palestinian president, Mahmoud Abbas, described the storming of the flotilla as a "massacre". The Palestinian chief negotiator, Saeb Erekat, described it as a "war crime".

Turkey, Spain and Greece demanded explanations from the Israeli ambassadors to their countries. Turkish police were sent to the residence of the Israeli ambassador in Ankara, which was surrounded by demonstrators. Nine of the dead activists were thought to be Turkish nationals.

Israel swiftly mounted a PR offensive to set out its version of events. The navy had promised to exercise restraint in dealing with the flotilla, and the bloodshed involved in the operation will inevitably leave Israel open to charges of excessive force.

The assault began at 4.30am in international waters, about 60 miles from the coast of Gaza where the convoy was heading to deliver its cargo of aid.

According to a spokeswoman for Israel Defence Forces (IDF), Avital Leibovich, officers aboard its warships gave the activists several warnings before boarding the Turkish ferry, the Mavi Marmara.

"We found ourselves in the middle of a lynching," she told reporters in the Israeli port of Ashdod. Around 10 activists attacked commandos, she said, relieving them of their pistols.

"We didn't look for confrontation but it was a massive attack," she said. "What happened was a last resort."

It was impossible to contact protesters on the ships, but the Free Gaza Movement, one of the organisers of the flotilla, said the IDF had started the violence, firing as soon as they boarded the ship.

At least one of the six boats in the flotilla arrived at lunchtime in Ashdod, 23-miles north of Gaza City. The port was closed to reporters, who took up position on a hill overlooking it.

Activists were expected to be processed in a large white tent on the quayside, where they would be offered the choice of immediate deportation to their country of origin or going through the lengthy process of the Israeli courts system.

The Israeli authorities gave no details of the injuries suffered by activists. It confirmed that 10 were dead, although government sources suggested the figure could be as high as 19. It claimed that one of its injured troops had suffered gunshot wounds and another had been stabbed.

Sheikh Raed Salah, the leader of the northern branch of the Islamic Movement, an influential organisation among Arab citizens of Israel, who was on board the Mavi Mamara, was also injured. There are conflicting reports as to the seriousness of his injuries.

The Swedish author Henning Mankell was on board one of the ships, which left Cyprus yesterday and had been due to arrive in Gaza today. The flotilla, which had been delayed by several days, was carrying around 650 activists and 10,000 tonnes of aid, including medical supplies and construction materials. The aim was to break the Israeli blockade of Gaza, which has been rigorously enforced for the past three years.

Leibovich defended Israel's action in international waters, saying it was permissible when a country's security was threatened.

Israel was expected to advise its nationals in Turkey to leave the country for fear of reprisals. A luxury liner, Magic 1, was diverted from the Turkish coast to Cyprus.

Abbas said: "What Israel has committed on board the freedom flotilla was a massacre." He declared three days of official mourning for the dead.

Israeli police cancelled leave and the army was on high alert, saying it feared possible rocket attacks from Islamist militants in Gaza and southern Lebanon.

Israel's deputy foreign minister, Danny Ayalon, described the activists as allies of Hamas and al-Qaida, claiming they would have opened an arms smuggling route to Gaza if they had been permitted to land there.